Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

REAPR: a universal tool for genome assembly evaluation

(2013) Martin Hunt et al.   GENOME BIOLOGY

Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly

(2012) H. Li   BIOINFORMATICS

Telescoper: de novo assembly of highly repetitive regions

(2012) Ma'ayan Bresler et al.   BIOINFORMATICS

Normalized N50 assembly metric using gap-restricted co-linear chaining

(2012) Veli Mäkinen et al.   BMC BIOINFORMATICS

Hybrid error correction and de novo assembly of single-molecule sequencing reads

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

De novo genome assembly: what every biologist should know

(2012) Monya Baker   NATURE METHODS

A beginner's guide to eukaryotic genome annotation

(2012) Mark Yandell et al.   NATURE REVIEWS GENETICS

Next-generation sequencing and large genome assemblies

(2012) Joseph Henson et al.   PHARMACOGENOMICS

Feature-by-Feature – Evaluating De Novo Sequence Assembly

(2012) Francesco Vezzi et al.   PLoS One

Reevaluating Assembly Evaluations with Feature Response Curves: GAGE and Assemblathons

(2012) Francesco Vezzi et al.   PLoS One

Next generation shotgun sequencing and the challenges of de novo genome assembly

(2012) Stephen Schlebusch et al.   SOUTH AFRICAN JOURNAL OF SCIENCE

Quake: quality-aware detection and correction of sequencing errors

(2012) David R Kelley et al.   GENOME BIOLOGY

Analysis of 2,440 human exomes highlights the evolution and functional impact of rare coding variation

(2012)   GENOME BIOLOGY

Genetic adaptation to high altitude in the Ethiopian highlands

(2012) Laura B Scheinfeldt et al.   GENOME BIOLOGY

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Assemblathon 1: A competitive assessment of de novo short read assembly methods

(2011) D. Earl et al.   GENOME RESEARCH

Efficient de novo assembly of large genomes using compressed data structures

(2011) J. T. Simpson et al.   GENOME RESEARCH

GAGE: A critical evaluation of genome assemblies and assembly algorithms

(2011) S. L. Salzberg et al.   GENOME RESEARCH

Dynamo maker ready to roll

(2011) Susan Young   NATURE

959 Nematode Genomes: a semantic wiki for coordinating sequencing projects

(2011) S. Kumar et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2012

(2011) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

Comparing De Novo Genome Assembly: The Long and Short of It

(2011) Giuseppe Narzisi et al.   PLoS One

De novo assembly of short sequence reads

(2010) K. Paszkiewicz et al.   BRIEFINGS IN BIOINFORMATICS

An overview of the current status of eukaryote gene prediction strategies

(2010) Roy D. Sleator   GENE

Assembly algorithms for next-generation sequencing data

(2010) Jason R. Miller et al.   GENOMICS

Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies

(2010) Sébastien Boisvert et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Haplotype-resolved genome sequencing of a Gujarati Indian individual

(2010) Jacob O Kitzman et al.   NATURE BIOTECHNOLOGY

Limitations of next-generation genome sequence assembly

(2010) Can Alkan et al.   NATURE METHODS

Assemblies: the good, the bad, the ugly

(2010) Ewan Birney   NATURE METHODS

High-resolution human genome structure by single-molecule analysis

(2010) B. Teague et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detection and correction of false segmental duplications caused by genome mis-assembly

(2010) David R Kelley et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species

(2009)   JOURNAL OF HEREDITY

The sequence and de novo assembly of the giant panda genome

(2009) Ruiqiang Li et al.   NATURE

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse

(2009) Deanna M. Church et al.   PLOS BIOLOGY

A Single Molecule Scaffold for the Maize Genome

(2009) Shiguo Zhou et al.   PLoS Genetics

De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae

(2008) J. A. Reinhardt et al.   GENOME RESEARCH

ALLPATHS: De novo assembly of whole-genome shotgun microreads

(2008) J. Butler et al.   GENOME RESEARCH

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Assessing the gene space in draft genomes

(2008) Genis Parra et al.   NUCLEIC ACIDS RESEARCH